Merge remote-tracking branch 'upstream/main' into tinylog

* upstream/main:
  Don't register any database changes to the indexer while dropping a file (#8334)
  Fix ACM fetcher (#8338)
  Squashed 'buildres/csl/csl-styles/' changes from 3bb4b5f..60bf7d5
  Exception shouldn't happen when pasting an entry with a publication date-range of form yyyy-yyyy (#8247)
  Refactor Sidepane logic (#8202)
  New translations JabRef_en.properties (Japanese) (#8331)
  Bump bcprov-jdk15on from 1.69 to 1.70 (#8333)
  Update Controlsfx to 11.1.1 (#8330)
  Update citeproc (#8329)
  Bump classgraph from 4.8.137 to 4.8.138 (#8327)
  Bump junit-platform-launcher from 1.8.1 to 1.8.2 (#8326)
  Remove outdated gradle deps check (#8324)
  Bump junit-jupiter from 5.8.1 to 5.8.2 (#8325)
  Bump libreoffice from 7.2.2 to 7.2.3 (#8328)
  Remove outdated ignores

.github/dependabot.yml

@@ -4,7 +4,7 @@ updates:
   directory: "/"
   schedule:
     interval: weekly
-  open-pull-requests-limit: 10
+  open-pull-requests-limit: 15
   labels:
   - "type: dependencies"
   ignore:
@@ -14,12 +14,6 @@ updates:
   - dependency-name: com.microsoft.azure:applicationinsights-logging-log4j2
     versions:
     - ">= 2.5.a" # Blocked by https://github.com/microsoft/ApplicationInsights-Java/issues/1155
-  - dependency-name: de.jensd:fontawesomefx-materialdesignfont
-    versions:
-    - "> 1.7.22-4" # Strange versioning format
-  - dependency-name: org.fxmisc.richtext:richtextfx
-    versions:
-    - "< 0.10.6" # Blocked by https://github.com/FXMisc/RichTextFX/issues/967, wait for new release
 - package-ecosystem: "github-actions"
   directory: "/"
   schedule:

CHANGELOG.md

@@ -41,6 +41,7 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We reworked the export order in the preferences and the save order in the library preferences. You can now set more than three sort criteria in your library preferences. [#7935](https://github.com/JabRef/jabref/pull/7935)
 - The metadata-to-pdf actions now also embeds the bibfile to the PDF. [#8037](https://github.com/JabRef/jabref/pull/8037)
 - The snap was updated to use the core20 base and to use lzo compression for better startup performance [#8109](https://github.com/JabRef/jabref/pull/8109)
+- We moved the union/intersection view button in the group sidepane to the left of the other controls. [#8202](https://github.com/JabRef/jabref/pull/8202)
 - We improved the Drag and Drop behavior in the "Customize Entry Types" Dialog [#6338](https://github.com/JabRef/jabref/issues/6338)
 - When determining the URL of an ArXiV eprint, the URL now points to the version [#8149](https://github.com/JabRef/jabref/pull/8149)
 - We Included all standard fields with citation key when exporting to Old OpenOffice/LibreOffice Calc Format [#8176](https://github.com/JabRef/jabref/pull/8176)
@@ -55,13 +56,16 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 
 ### Fixed
 
+- We fixed an issue where an exception occurred when pasting an entry with a publication date-range of the form 1910/1917 [#7864](https://github.com/JabRef/jabref/issues/7864)
 - We fixed an issue where an exception occured when a preview style was edited and afterwards another preview style selected. [#8280](https://github.com/JabRef/jabref/issues/8280)
 - We fixed an issue where the actions to move a file to a directory were incorrectly disabled. [#7908](https://github.com/JabRef/jabref/issues/7908)
 - We fixed an issue where an exception occurred when a linked online file was edited in the entry editor [#8008](https://github.com/JabRef/jabref/issues/8008)
 - We fixed an issue when checking for a new version when JabRef is used behind a corporate proxy. [#7884](https://github.com/JabRef/jabref/issues/7884)
 - We fixed some icons that were drawn in the wrong color when JabRef used a custom theme. [#7853](https://github.com/JabRef/jabref/issues/7853)
 - We fixed an issue where the `Aux file` on `Edit group` doesn't support relative sub-directories path to import. [#7719](https://github.com/JabRef/jabref/issues/7719).
 - We fixed an issue where it was impossible to add or modify groups. [#7912](https://github.com/JabRef/jabref/pull/793://github.com/JabRef/jabref/pull/7921)
+- We fixed an issue about the visible side pane components being out of sync with the view menu. [#8115](https://github.com/JabRef/jabref/issues/8115)
+- We fixed an issue where the side pane would not close when all its components were closed. [#8082]((https://github.com/JabRef/jabref/issues/8082))
 - We fixed an issue where exported entries from a Citavi bib containing URLs could not be imported [#7892](https://github.com/JabRef/jabref/issues/7882)
 - We fixed an issue where the icons in the search bar had the same color, toggled as well as untoggled. [#8014](https://github.com/JabRef/jabref/pull/8014)
 - We fixed an issue where typing an invalid UNC path into the "Main file directory" text field caused an error. [#8107](https://github.com/JabRef/jabref/issues/8107)
@@ -75,6 +79,8 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
 - We fixed an issue where an exception would occur when clicking on a DOI link in the preview pane [#7706](https://github.com/JabRef/jabref/issues/7706)
 - We fixed an issue where XMP and embedded BibTeX export would not work [#8278](https://github.com/JabRef/jabref/issues/8278)
 - We fixed an issue where the XMP and embedded BibTeX import of a file containing multiple schemas failed [#8278](https://github.com/JabRef/jabref/issues/8278)
+- We fixed an issue where pdf-paths and the pdf-indexer could get out of sync [#8182](https://github.com/JabRef/jabref/issues/8182)
+
 
 ### Removed
 

build.gradle

@@ -14,8 +14,6 @@ plugins {
 
     id 'me.champeau.gradle.jmh' version '0.5.3'
 
-    id 'com.github.ben-manes.versions' version '0.39.0'
-
     id 'org.javamodularity.moduleplugin' version '1.8.10'
 
     id 'org.openjfx.javafxplugin' version '0.0.10'
@@ -126,11 +124,11 @@ dependencies {
     implementation group: 'org.apache.tika', name: 'tika-core', version: '2.1.0'
 
     // required for reading write-protected PDFs - see https://github.com/JabRef/jabref/pull/942#issuecomment-209252635
-    implementation 'org.bouncycastle:bcprov-jdk15on:1.69'
+    implementation 'org.bouncycastle:bcprov-jdk15on:1.70'
 
     implementation 'commons-cli:commons-cli:1.5.0'
 
-    implementation 'org.libreoffice:libreoffice:7.2.2'
+    implementation 'org.libreoffice:libreoffice:7.2.3'
     implementation 'org.libreoffice:unoloader:7.2.2'
 
     implementation 'io.github.java-diff-utils:java-diff-utils:4.11'
@@ -173,7 +171,7 @@ dependencies {
     implementation 'org.fxmisc.richtext:richtextfx:0.10.7'
     implementation group: 'org.glassfish.hk2.external', name: 'jakarta.inject', version: '2.6.1'
     implementation 'com.jfoenix:jfoenix:9.0.10'
-    implementation 'org.controlsfx:controlsfx:11.1.0'
+    implementation 'org.controlsfx:controlsfx:11.1.1'
 
     implementation 'org.jsoup:jsoup:1.14.3'
     implementation 'com.konghq:unirest-java:3.13.4'
@@ -183,7 +181,7 @@ dependencies {
     implementation "org.tinylog:slf4j-tinylog:2.4.1"
     implementation "org.tinylog:tinylog-impl:2.4.1"
 
-    implementation 'de.undercouch:citeproc-java:3.0.0-alpha.2'
+    implementation 'de.undercouch:citeproc-java:3.0.0-alpha.3'
 
     implementation group: 'jakarta.activation', name: 'jakarta.activation-api', version: '1.2.1'
     implementation group: 'jakarta.xml.bind', name: 'jakarta.xml.bind-api', version: '2.3.2'
@@ -204,9 +202,9 @@ dependencies {
 
     implementation group: 'net.harawata', name: 'appdirs', version: '1.2.1'
 
-    testImplementation 'io.github.classgraph:classgraph:4.8.137'
-    testImplementation 'org.junit.jupiter:junit-jupiter:5.8.1'
-    testImplementation 'org.junit.platform:junit-platform-launcher:1.8.1'
+    testImplementation 'io.github.classgraph:classgraph:4.8.138'
+    testImplementation 'org.junit.jupiter:junit-jupiter:5.8.2'
+    testImplementation 'org.junit.platform:junit-platform-launcher:1.8.2'
 
     testRuntimeOnly group: 'org.apache.logging.log4j', name: 'log4j-core', version: '3.0.0-SNAPSHOT'
     testRuntimeOnly group: 'org.apache.logging.log4j', name: 'log4j-jul', version: '3.0.0-SNAPSHOT'
@@ -223,46 +221,6 @@ dependencies {
     xjc group: 'org.glassfish.jaxb', name: 'jaxb-xjc', version: '2.3.3'
 }
 
-dependencyUpdates {
-    outputFormatter = "json"
-}
-
-// We have some dependencies which cannot be updated due to various reasons.
-dependencyUpdates.resolutionStrategy {
-    componentSelection { rules ->
-        rules.all { ComponentSelection selection ->
-            boolean rejected = ['alpha', 'snapshot', 'beta', 'rc', 'cr', 'm', 'preview', 'b', 'ea'].any { qualifier ->
-                selection.candidate.version ==~ /(?i).*[.-]$qualifier[.\d-+]*/
-            }
-            if (rejected) {
-                selection.reject('Release candidate')
-            }
-        }
-        rules.withModule("org.javamodularity.moduleplugin:org.javamodularity.moduleplugin.gradle.plugin") { ComponentSelection selection ->
-            if (selection.candidate.version ==~ /1.6.0/) {
-                selection.reject("Does not work due to bug, see https://github.com/JabRef/jabref/pull/5270")
-            }
-        }
-        rules.withModule("com.microsoft.azure:applicationinsights-core") { ComponentSelection selection ->
-            if (selection.candidate.version ==~ /2.5.0/ || selection.candidate.version ==~ /2.5.1/) {
-                selection.reject("Does not work due to bug, see https://github.com/JabRef/jabref/pull/5596")
-            }
-        }
-        rules.withModule("com.microsoft.azure:applicationinsights-logging-log4j2") { ComponentSelection selection ->
-            if (selection.candidate.version ==~ /2.5.0/ || selection.candidate.version ==~ /2.5.1/) {
-                selection.reject("Does not work due to bug, see https://github.com/JabRef/jabref/pull/5596")
-            }
-        }
-    }
-}
-
-task checkOutdatedDependencies(dependsOn: dependencyUpdates) {
-    doLast {
-        def dependencyReport = new JsonSlurper().parseText(new File("build/dependencyUpdates/report.json").text)
-        assert dependencyReport.outdated.count == 0: "There are outdated dependencies in build.gradle!\n Run ./gradlew dependencyUpdates to see which"
-    }
-}
-
 clean {
     delete "src/main/generated"
     delete "src-gen"